Dockerized web workflow tries to run directly if "Edit XML" or "Advanced Edit"

[ashiklom]

Describe the bug
Using the Dockerized web interface -- if the user tries to edit the PEcAn XML through the web interface, the web container tries to execute the workflow itself (i.e. by calling $Rbinary) rather than posting a message to RabbitMQ to trigger the executor container. This silently fails (i.e. web workflow hangs) because none of the required components (including R itself) are available on the web container.

To Reproduce
Steps to reproduce the behavior:

1. Run the Dockerized PEcAn web workflow.
2. Select "Edit PEcAn XML"
3. Save the XML and try to proceed with the workflow.

The "Job executing" page should hang with no output. A tiny little message in the web container logs will show something like sh: /usr/bin/R not found.

Expected behavior
Web container should post a message to RabbitMQ after PEcAn edit, which will be picked up by the executor and the workflow will proceed as before.

Machine (please complete the following information):
PEcAn Docker.

Proposed solution

Add the RabbitMQ submission code from 04-runpecan.php to whatever happens after pecan_edit, model_edit, etc.
As a band-aid, this can be copy-pasted, but a better solution would involve writing a PHP function (in common.php) to send a RabbitMQ message, which can then be re-used more easily.

[ashiklom]

Looking more closely, looks like the problematic script is 07-continue.php, which has this at the very bottom:

# check if we edited pecan.xml
if (file_exists($folder . DIRECTORY_SEPARATOR . "STATUS")) {
  # add end of advanced edit
  $fh = fopen($folder . DIRECTORY_SEPARATOR . "STATUS", 'a') or die("can't open file");
  fwrite($fh, "\t" . date("Y-m-d H:i:s") . "\tDONE\t\n");
  fclose($fh);

  $exec .= " --continue workflow.R workflow2.Rout";
} else {
  if ($model_edit) {
    $exec .= " --advanced";
  }
  $exec .= " workflow.R";
}

# start the workflow again
chdir($folder);
pclose(popen("$exec &", 'r'));

All of this should probably be wrapped in a if (host != "rabbitmq") and an additional condition for host = "rabbitmq" should be added.

[ashiklom]

Bigger picture -- It might be worth revising the executor container's RabbitMQ receiver/consumer script to allow it to take arbitrary commands. Then, we would be able to pass the $exec statements peppered through the web interface directly to that container if RabbitMQ is running.

I.e. Use the PHP code to craft a message like:

$message = '{"custom_command": "' . $exec . '"}'

...which would expand to...

{"custom_command": "$R_LIBS_USER=/path/to/R/library /usr/bin/R CMD BATCH --continue workflow.R workflow2.Rout"}

Then, the Docker receiver can just have a special case for the raw command:

default_application = os.getenv('APPLICATION', 'job.sh')
# ...
custom_application = jbody.get('custom_application')
if custom_application is not None:
    application = custom_application
else:
    application = default_application
# Proceed with current logic...